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Molecular architecture of the chikungunya virus replication complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DOP
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.4093 f_angle_d 0.507 f_chiral_restr 0.0406 f_plane_restr 0.0048 f_bond_d 0.002
Sample Alphavirus Replication Complex Sample Components nsP1 dodecameric ring nsP4 RdRp; docked within nsP1 central cavity nsP2 helicase-protease; docked on top of viral complex with synthetic RNA bound
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details wait 45s, blot 2s at force -2
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 132510 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7DOP) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation Coefficient Overall B Value 63.66 Fitting Procedure Details ChimeraX was used to fit the 7DOP ring and built/refined using coot/phenix.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 34
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 1600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.1 PARTICLE SELECTION Topaz 2.5.0 IMAGE ACQUISITION EPU 2.14 CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF ChimeraX 1.3 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.2 MODEL REFINEMENT Coot 0.9.5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2261181 template-based picking and neural-network trained TOPAZ picking